Well, there are two thigns you're talking about. One is constantly referring to Obama as "Barack Hussein Obama" to bring up his middle name to scare people into thinking he's Muslim when he's not. When the right-wingers constantly mention his misleading middle name, it is done so in bad faith to imply that he's something he is not.
But as for a general dislike/distrust of Islamic people, I find that perfectly acceptable as Muslims have declared war against America. Yeah yeah, "not all" Muslims but enough of them to be more than a significant amount, and even the ones who are not on a Jihad against The Great Satan America stay quiet when other Muslims are badmouthing America.
Yeah yeah, you might find some occasional people who claim they are Muslims and say the don't hate America, but it's always someone who lives in America (probably a white guy or black guy who converted to Islam in prison), and they're either not a real Muslim (in the same way a Christian who supports abortion rights, the freedom to not be a Christian, and goes to church once a year is not a real Christian), or they're just flat out lying to provide an example of a Muslim who doesn't hate America. In private, when talking with other Muslims, they sure as stinky crap hate America.
But the bigger point is that there is a big difference between hating someone because of a physical/geographical trait they were born with and had no choice in, such as skin color, race, or nationality. But religions are belief systems. It's true that people are born into them and have no choice in whether they get brainwashed by one religion over another, but they can still take steps to cure themselves of it if they are so inclined. The same is not true for what race you are or in what country you were born.
There is nothing wrong with hating/disliking/fearing/etc (collectively "to be bigoted against") a person because of the things they believe. It's perfectly acceptable to be bigoted against Nazis and white supremacists and KKK members. Those are ways of thinking, not physical traits. Religions are no different, except racist groups are honest about what they are while religions pretend to stand for morality. I'd rather be in a room full of KKK members than a room full of Muslims (or evangelical Christians or radical Jews), as I could have a more rational discussion with the KKK members than the religious people, and I'd feel that I'd be more likely to be killed by the religious people than the KKK people. But I can't stand all of them.
All real Muslims hate America, because the Koran says they have to, all their top leaders have issued fatwas and jihads and every possible order and declaration that America is evil and the enemy of Islam and is to be destroyed. Just as Catholics have to listen to the Pope, Muslims have to listen to the Imams. And yes, I'm grouping them all together. The Koran is the Koran, whether the're Sunni or Shit-ites. They can kill each other all the want, but the one thing on which they agree is that America is the Great Satan. They all hate Israel and America supports, arms, funds, and defends Israel. So any true Muslim hates America. I don't care if they get some white guy on the news claiming to be a Muslim and claiming to not hate America and spewing some bullshit about how "only a small minority of Muslims hate America blah blah blah Islam is a religion of peace blah blah blah" - bullshit. And Republicans care about freedom, liberty, and working people while Democrats care about fiscal responsibility and small government. Bullshit bullshit bullshit. It doesn't matter what people say, it matters how they act. And it's perfectly acceptable to loathe and despise someone, or a large group of people, for how they act and what they believe in. It's not, however, okay to hate someone over physical traits they had no choice in bringing about. Some bigotry is okay, some is not.